knitr document van Steensel lab

TF reporter barcode processing - pMT02 - stimulation 2

Introduction

18,000 TF reporters on pMT02 were transfected into mESCs (in total 10 different conditions), sequencing data yielded barcode counts of these experiments. These counts will be processed in this script.

Analysis

Add barcode annotation to barcode counts & extract first bc read count information

Data quality plots

Normalization of barcode counts:

Divide cDNA barcode counts through pDNA barcode counts to get activity

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Calculate mean activity - filter out outlier barcodes

Calculate correlations between technical replicates

Data quality plots - correlation between replicates

Session Info

paste("Run time: ",format(Sys.time()-StartTime))
## [1] "Run time:  8.483114 mins"
getwd()
## [1] "/DATA/usr/m.trauernicht/projects/SuRE-TF/gen-1_stimulation-2"
date()
## [1] "Thu Nov 26 09:42:59 2020"
sessionInfo()
## R version 3.6.3 (2020-02-29)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.7 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/libblas/libblas.so.3.6.0
## LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] parallel  stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] gridExtra_2.3       RColorBrewer_1.1-2  readr_1.3.1        
##  [4] haven_2.2.0         ggbeeswarm_0.6.0    plotly_4.9.2.1     
##  [7] tibble_3.0.1        dplyr_0.8.5         vwr_0.3.0          
## [10] latticeExtra_0.6-29 lattice_0.20-38     stringdist_0.9.5.5 
## [13] GGally_1.5.0        ggpubr_0.2.5        magrittr_1.5       
## [16] ggplot2_3.3.0       stringr_1.4.0       plyr_1.8.6         
## [19] data.table_1.12.8  
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.5        tidyr_1.0.0       png_0.1-7         assertthat_0.2.1 
##  [5] digest_0.6.27     mime_0.9          R6_2.5.0          evaluate_0.14    
##  [9] httr_1.4.1        pillar_1.4.3      rlang_0.4.8       lazyeval_0.2.2   
## [13] Matrix_1.2-18     rmarkdown_2.5     splines_3.6.3     labeling_0.3     
## [17] htmlwidgets_1.5.2 munsell_0.5.0     shiny_1.4.0       compiler_3.6.3   
## [21] vipor_0.4.5       httpuv_1.5.4      xfun_0.19         pkgconfig_2.0.3  
## [25] mgcv_1.8-31       htmltools_0.5.0   tidyselect_1.1.0  reshape_0.8.8    
## [29] viridisLite_0.3.0 later_1.1.0.1     crayon_1.3.4      withr_2.1.2      
## [33] grid_3.6.3        nlme_3.1-143      xtable_1.8-4      jsonlite_1.7.1   
## [37] gtable_0.3.0      lifecycle_0.2.0   scales_1.1.0      stringi_1.5.3    
## [41] farver_2.0.1      ggsignif_0.6.0    reshape2_1.4.4    promises_1.1.1   
## [45] ellipsis_0.3.0    vctrs_0.2.4       tools_3.6.3       forcats_0.4.0    
## [49] glue_1.4.2        beeswarm_0.2.3    purrr_0.3.3       hms_0.5.3        
## [53] crosstalk_1.0.0   jpeg_0.1-8.1      prettydoc_0.4.0   fastmap_1.0.1    
## [57] yaml_2.2.1        colorspace_1.4-1  knitr_1.30